Computational model uncovers progression of HIV infection in brain

University of Alberta research team successfully uncovered the progression of HIV infection in the brain using a new mathematical model. The team is utilizing this model to develop a nasal spray to administer  antiretroviral medication effectively. Their research is published in Journal of Neurovirology.

Research was done by PhD student Weston Roda and Prof. Michael Li. They used data from patients who died five to 15 years after they were infected, as well as known biological processes for the HIV virus to build the model that predicts the growth and progression of HIV in the brain, from the moment of infection onward. It is the first model of an infectious disease in the brain.

“The nature of the HIV virus allows it to travel across the blood-brain barrier in infected macrophage–or white blood cell–as early as two weeks after infection. Antiretroviral drugs, the therapy of choice for HIV, cannot enter the brain so easily,” said Roda. This creates what is known as a viral reservoir, a place in the body where the virus can lay dormant and is relatively inaccessible to drugs.

Prior to this study, scientists could only study brain infection at autopsy. The new model allows scientists to backtrack, seeing the progression and development of HIV infection in the brain. Using this information, researchers can determine what level of effectiveness is needed for antiretroviral therapy in the brain to decrease active infection.

“The more we understand and can target treatment toward viral reservoirs, the closer we get to developing total suppression strategies for HIV infection,” said Roda. A research team led by Chris Power, Roda’s co-supervisor who is a professor in the Division of Neurology, is planning clinical trials for a nasal spray that would get the drugs into the brain faster, with critical information on dosage and improvement rate provided by Roda’s model.

“Our next steps are to understand other viral reservoirs, like the gut, and develop models similar to this one, as well as understand latently infected cell populations in the brain,” said Roda. “With the antiretroviral therapy, infected cells can go into a latent stage. The idea is to determine the size of the latently infected population so that clinicians can develop treatment strategies”

Citation: Roda, Weston C., Michael Y. Li, Michael S. Akinwumi, Eugene L. Asahchop, Benjamin B. Gelman, Kenneth W. Witwer, and Christopher Power. “Modeling brain lentiviral infections during antiretroviral therapy in AIDS.” Journal of NeuroVirology, 2017.
Adapted from press release by University of Alberta.

Researchers identify how Ebola virus disables the human immune system

A research study by scientists at the University of Texas Medical Branch in Galveston sheds light on how Ebola effectively disables the human immune system. Virologist Alex Bukreyev, UTMB professor and senior author of the study, said the research team engineered versions of the Ebola virus in order to understand its effects on immune system. The findings are described in journal PLOS Pathogens.

Previous research shown how Ebola virus inhibits Interferon mediated immune defense system. Interferons are specialized signaling proteins that are made and released in response to an invasion by a virus or other pathogen, which directly inhibit replication of viral particles in cells. These actions were mediated by two protein regions within the Ebola virus’ structure called interferon inhibiting domains, or IIDs, that prevent the host’s interferons from doing their job thus disabling the host’s immune system defenses.

A focus of current research has been how Ebola gets around the host’s cell-mediated immune response, which is another defense mechanism involving some specialized immune cells that either kill virus-infected cells or secrete antibodies that directly neutralize the virus. Researchers assessed role played by interferon inhibiting domains (IID’s) on cell mediated immunity.

The study used genetically altered strains of the Ebola virus that were designed with one or both of the interferon inhibiting domains disabled to study what they do to the host. The altered viruses were placed on specific types of immune cells isolated from human blood, called dendritic cells, T lymphocytes, B lymphocytes and natural killer cells, as these types of cells are key players in marshaling defenses.

“We found that interferon inhibiting domains work not only in ways previously established, which includes interference in cascades of protective biochemical reactions that occur in cells in response to Ebola that limit infection”, Bukreyev said. “The IID’s also counter the activity of immune cells, including T lymphocytes and natural killer cells that kill virus-infected cells as well as B lymphocytes that secrete antibodies.” “It’s a double edged sword – the IIDs not only block interferon signaling, they also prevent infected cells from activating the cell-mediated arm of the immune response,” said Patrick Younan, research scientist and co-lead author of the paper.

Citation: Lubaki, Ndongala Michel, Patrick Younan, Rodrigo I. Santos, Michelle Meyer, Mathieu Iampietro, Richard A. Koup, and Alexander Bukreyev. “The Ebola Interferon Inhibiting Domains Attenuate and Dysregulate Cell-Mediated Immune Responses.” PLOS Pathogens 12, no. 12 (2016).
Adapted from press release by the University of Texas Medical Branch at Galveston.

Analysis of interactome of Zika virus infected neural cells shows altered expression of more than 500 proteins

Zika virus (ZIKV) interferes with the cellular machinery controlling cell division and alters the expression of hundreds of genes responsible for guiding the formation and development of brain cells, according to findings of research published in Scientific Reports.

Zika virus wikipedia
Zika virus structure. Credit: Wikipedia / David Goodwill

The association between Zika virus (ZIKV) infection and microcephaly has been previously established. Nevertheless, the cellular changes caused by the virus and leading to microcephaly are largely unknown. “Elucidating the foundations of Zika virus infection is crucial in order to develop tools against it”, says Stevens Rehen, the principal investigator of the study and a researcher working at the D’ Or Institute for Research and Education (IDOR) and at the Institute of Biomedical Sciences at Federal University of Rio de Janeiro (UFRJ) in Brazil.

In a previous study published by the group in Science magazine, researchers observed that the pool of human neural stem cells infected by the Brazilian strain of Zika virus was rapidly and completely depleted if compared to non-infected cells. This finding led the group to further investigate how Zika virus disrupts the interactome map (or molecular fingerprinting) of infected cells – which is the entire set of cellular and molecular interactions in a given cell group. The analysis of the interactome of Zika-infected cells may reveal the cellular targets and pathways with which the virus interacts or which it modulates, offering valuable opportunities for drug design.

To this end, human neural cells were infected by a strain of Zika virus (ZIKV) obtained from a Brazilian patient. These cells were then made into neurospheres, which are organized 3D aggregates of neural cells resembling fetal brain tissue that recapitulate many of the normal early and crucial processes that the brain undergoes through development and thus are a great model for studying the human brain. Next, the group identified the molecular fingerprinting of infected and non-infected cells by checking the expression level and status of innumerous genes and proteins.

The analysis revealed that more than 500 proteins in infected neurospheres had their expression level or status (upregulated vs downregulated) altered, if compared to non-infected neurospheres. A number of these altered proteins are normally involved with tasks such as fixing DNA damage or assuring chromosomal stability. Also, proteins that are normally required for cell growth were silent in infected neurospheres, which may explain why Zika-infected cells die much sooner than their non-infected counterparts. Interestingly, genes driving cell specialization were also silent in infected neurospheres, precluding that specialized brain cells were generated. On the other hand, proteins associated with viral replication were over-abundant, most likely the result of a strategy adopted by the virus to promote its own replication in the host cell. A complete list of all human proteins that have been found altered in Zika-infected neurospheres is available in the study entitled “Zika virus disrupts molecular fingerprinting of human neurospheres”, published in Scientific Reports this week. 

According to Patricia Garcez, Assistant Professor at the Federal University of Rio de Janeiro and the first author of the study: “these findings provide insights into the molecular mechanisms of Zika virus (ZIKV) infection over the course of brain development and may explain some of the consequences seen in the brain of newborns with microcephaly”.

Citation: Patricia P. Garcez, Juliana Minardi Nascimento, Janaina Mota de Vasconcelos, Rodrigo Madeiro da Costa, Rodrigo Delvecchio, Pablo Trindade, Erick Correia Loiola, Luiza M. Higa, Juliana S. Cassoli, Gabriela Vitória, Patricia C. Sequeira, Jaroslaw Sochacki, Renato S. Aguiar, Hellen Thais Fuzii, Ana M. Bispo de Filippis, João Lídio da Silva Gonçalves Vianez Júnior, Amilcar Tanuri, Daniel Martins-de-Souza & Stevens K. Rehen. “Zika virus disrupts molecular fingerprinting of human neurospheres.” Scientific Reports 7, Article number: 40780 (2017).
DOI: 10.1038/srep40780
Research funding: Brazilian Development Bank, Funding Authority for Studies and Projects, National Council of Scientific and Technological Development, Foundation for Research Support – State of Rio de Janeiro, São Paulo Research Foundation.
Adapted from press release by D’ Or Institute for Research and Education (IDOR).

New plant based compounds show promise for hepatitis B

Researchers have found that certain plant-derived products may help prevent and treat hepatitis B virus (HBV) infection. Proanthocyanidin (PAC) and its analogs, oolonghomobisflavanes, act by inhibiting viral entry into host cells.

Hepatis B life cycle
The life cycle of Hepatitis B Virus. Credit Dr. Graham Colm Wikipedia

The investigators noted that PAC was effective even against treatment-resistant HBV strains, and it augmented the ability of the antiviral drug tenofovir to interrupt HBV spread in human cells.

“PAC represents a specific inhibitor against HBV that is a less toxic plant-derived agent used as a dietary supplement,” said Dr. Koichi Watashi, co-author of the Hepatology study.

Senko Tsukuda, Koichi Watashi, Taichi Hojima, Masanori Isogawa, Masashi Iwamoto, Katsumi Omagari, Ryosuke Suzuki, Hideki Aizaki, Soichi Kojima, Masaya Sugiyama, Akiko Saito, Yasuhito Tanaka, Masashi Mizokami, Camille Sureau and Takaji Wakita. “A new class of hepatitis B and D virus entry inhibitors, proanthocyanidin and its analogs, that directly act on the viral large surface proteins.” Hepatology 2017.
DOI: 10.1002/hep.28952
Adapted from press release by Wiley Publications.

Role of retroviruses in evolution of human brain

Over millions of years, retroviruses have been incorporated into our human DNA, where they today make up almost 10 percent of the total genome. A research group at Lund University in Sweden has now discovered a mechanism through which these retroviruses may have an impact on gene expression. This means that they may have played a significant role in the development of the human brain as well as in various neurological diseases.

Retroviruses are a special group of viruses including some which are dangerous, such as HIV, while others are believed to be harmless. The viruses studied by Johan Jakobsson and his colleagues in Lund are called endogenous retroviruses (ERV) as they have existed in the human genome for millions of years. They can be found in a part of DNA that was previously considered unimportant, so-called junk-DNA a notion that researchers have now started to reconsider.

The genes that control the production of various proteins in the body represent a smaller proportion of our DNA than endogenous retroviruses. They account for approximately 2 per cent, while retroviruses account for 8-10 per cent of the total genome. If it turns out that they are able to influence the production of proteins, this will provide us with a huge new source of information about the human brain”, says Johan Jakobsson.

And this is precisely what the researchers discovered. They have determined that several thousands of the retroviruses that have established themselves in our genome may serve as “docking platforms” for a protein called TRIM28. This protein has the ability to “switch off” not only viruses but also the standard genes adjacent to them in the DNA helix, allowing the presence of ERV to affect gene expression.

This switching-off mechanism may behave differently in different people since retroviruses are a type of genetic material that may end up in different places in the genome. This makes it a possible tool for evolution, and even a possible underlying cause of neurological diseases. In fact, there are studies that indicate a deviating regulation of ERV in several neurological diseases such as ALS, schizophrenia, and bipolar disorder.

Two years ago, Johan Jakobsson’s team showed that ERV had a regulatory role in neurons specifically. However, this study was conducted on mice, whereas the new study published in the journal Cell Reports was made using human cells.

The differences between mice and humans are particularly important in this context. Many of the retroviruses that have been built into the human DNA do not exist in species other than humans and our closest relatives gorillas and chimpanzees. They seem to have incorporated themselves into the genome some 35-45 million years ago when the evolutionary lineage of primates was divided between the Old and New World.

“Much of what we know about the overall development of the brain comes from the fruit fly, zebrafish, and mouse. However, if endogenous retroviruses affect brain function, and we have our own set of these ERV, the mechanisms they affect may have contributed to the development of the human brain”, says Johan Jakobsson.

Citation: Brattås, Per Ludvik, Marie E. Jönsson, Liana Fasching, Jenny Nelander Wahlestedt, Mansoureh Shahsavani, Ronny Falk, Anna Falk, Patric Jern, Malin Parmar, Johan Jakobsson. “TRIM28 Controls a Gene Regulatory Network Based on Endogenous Retroviruses in Human Neural Progenitor Cells.” Cell reports Volume 18, Issue 1, p1–11.
DOI: 10.1016/j.celrep.2016.12.010
Adapted from press release by Lund University.

Researchers use computer simulation to understand structure of virus

(Pittsburg) Researchers led by Carnegie Mellon University physicist Markus Deserno and University of Konstanz (Germany) chemist Christine Peter have developed a computer simulation that crushes viral capsids. By allowing researchers to see how the tough shells break apart, the simulation provides a computational window for looking at how viruses and proteins assemble. The study is published in the October issue of The European Physical Journal Special Topics.

Computer simulation of Cowpea Chlorotic Mottle Virus (CCMV) capsid.
Credit: Venkatramanan Krishnamani

Viral capsids, the protein shells that encapsulate and transport the viral genome, are one of nature’s strongest nanocontainers. The shells are made when copies of capsid proteins spontaneously come together and assemble into a round, geometric shell. Understanding how these proteins come together to form capsids may help researchers to make similar nanocontainers for a variety of uses, including targeted drug delivery. Additionally, the simulation could fill a void for virologists, allowing them to study the stages of viral assembly that they aren’t able to see experimentally.

Studying the self-assembly of viral capsids is difficult. Most viruses are too small — about 30 to 50 nanometers — and the capsid proteins come together too rapidly for their assembly to be seen using traditional microscopy. As an alternative, Deserno and colleagues thought that a better way to learn about capsid assembly might be to see what happens when an already formed capsid breaks apart.

To do this, Deserno and colleagues created a coarse-grained model of the Cowpea Chlorotic Mottle Virus (CCMV) capsid. In the simulation, they applied forces to the capsid and viewed how it responded to those forces. Their model is based on the MARTINI force field, a commonly used coarse-grained model, with an added stabilizing network within the individual proteins that compensated for the model’s shortcomings in stabilizing a protein’s folding geometry.

The Cowpea Chlorotic Mottle Virus capsid is made up of 180 identical proteins. In assembly, the proteins first form pairs, called dimers, and those dimers then join together at interfaces. While the proteins are the same, the interfaces can be different. At some locations on the capsid, five proteins meet; at others, six. In the simulation, the researchers found that when force was applied to the capsid, the capsid would start to fracture at the hexametric interfaces first, indicating that those protein-protein contacts were weaker than those at the pentametric interfaces. In contrast, the pentametric contacts never broke. Since stronger connections assemble first and weaker ones assemble later, the researchers can use this information to begin to recreate how the capsid formed.

In the simulation, the researchers also found a likely explanation for a strange structural feature found in the Cowpea Chlorotic Mottle Virus capsid. At the center of the hexametric association site, the tail-ends of the six proteins come together and form a beta barrel. Beta barrels are coiled secondary protein structures. The researchers believe that they act to provide further late-stage stabilization to the weaker hexametric interfaces.

Publication: Breaking a virus: Identifying molecular level failure modes of a viral capsid by multiscale modeling.
Journal: The European Physical Journal Special Topics
Adapted from press release by Carnegie Mellon University